The problem is the rule of primacy. If I learned how to clear my mask while kneeling, and I'm having difficulty with it, I'm going to return to the way I first learned it. I saw this in the Keys all the time. You would see divers stop and kneel on the reef in order to clear their mask. When you teach skills while kneeling you're introducing them to a horrible bad habit. Many never grow out of it.
When you teach all the skills on the knees, the student really has to learn it twice. Many of the skills are markedly different while vertical than when horizontal. Sometimes you don't even notice the difference, but it confuses the hell out of the student. I had been teaching all horizontal for a while when someone asked me how I "did" it. The question floored me. My response was in effect: "don't effin kneel". But over the years, I really see the differences between the two.
Finally, it's a matter of comfort. Every minute you have your student practicing trim and neutral is less effort you'll have to exert managing them. It seemed that almost every class had a "bolter". You know, that one student who panics and tries to bolt to the surface? Here's a clue: they're not comfortable. They're not comfortable because they're not in control. They're not in control because, in many classes, neutral buoyancy is the last skill introduced in the pool. Since I eliminated kneeling, I haven't had a single bolter. My class is under complete control.
I have not had a student who couldn't hover on the first day. Most can do it after the first hour.I take two three//four hour sessions to train a diver to the point I'll trust them in OW. It doesn't take magic. It doesn't take being a superior instructor. It simply takes a commitment to do it.